scglue: test-2

scripts/download_resources_test.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+set -e
+
+echo ">> Downloading resources"
+
+viash run src/common/sync_test_resources/config.vsh.yaml -- \
+  --input "s3://openproblems-data/resources_test/grn/" \
+  --output "resources_test" \
+  --delete
+
+

src/api/file_multiomics_atac_h5ad.yaml

@@ -1,5 +1,5 @@
 type: file
-example: resources_test/grn-benchmark/multiomics_atac.h5ad
+example: resources/grn-benchmark/multiomics_atac.h5ad
 info:
   label: multiomics atac
   summary: "Peak data for multiomics data."

src/api/file_multiomics_rna_h5ad.yaml

@@ -1,5 +1,5 @@
 type: file
-example: resources_test/grn-benchmark/multiomics_rna.h5ad
+example: resources/grn-benchmark/multiomics_rna.h5ad
 info:
   label: multiomics rna
   summary: "RNA expression for multiomics data."

src/methods/scglue/config.novsh.yaml → src/methods/dummy/config.novsh.yaml

@@ -1,13 +1,14 @@
 __merge__: ../../api/comp_method.yaml
 
 functionality:
-  name: scglue
+  name: dummy
   info:
-    label: scglue
-    summary: "GRN inference using scglue"
+    label: dummy
+    summary: "FILL IN: A one sentence summary of this method."
     description: |
-      GRN inference using scglue. 
-    documentation_url: https://scglue.readthedocs.io/
+      A dummy method that contains the format of a real GRN inference method.
+    documentation_url: https://url.to/the/documentation
+    repository_url: https://github.com/organisation/repository
   arguments:
     - name: --multiomics_rna
       __merge__: ../../api/file_multiomics_rna_h5ad.yaml
@@ -62,20 +63,17 @@ functionality:
       type: integer
       direction: input
       default: 4
-      
+
   resources:
     - type: python_script
       path: script.py
-    - path: main.py
 
 platforms:
   - type: docker
-    image: nvcr.io/nvidia/pytorch:24.06-py3
+    image: ghcr.io/openproblems-bio/base_python:1.0.4
     setup:
       - type: python
-        packages: [ scglue==0.3.2, pyscenic==0.12.1, numpy==1.23.4, scanpy, networkx, pyarrow, cytoolz, scikit-misc, cuda-python]
-      - type: apt
-        packages: [bedtools]
+        packages: [  ]
 
   - type: native
   - type: nextflow

src/methods/dummy/config.vsh.yaml → src/methods/scglue/config.vsh.yaml

@@ -1,14 +1,13 @@
-# __merge__: ../../api/comp_method.yaml
+__merge__: ../../api/comp_method.yaml
 
 functionality:
-  name: dummy
+  name: scglue
   info:
-    label: dummy
-    summary: "FILL IN: A one sentence summary of this method."
+    label: scglue
+    summary: "GRN inference using scglue"
     description: |
-      A dummy method that contains the format of a real GRN inference method.
-    documentation_url: https://url.to/the/documentation
-    repository_url: https://github.com/organisation/repository
+      GRN inference using scglue. 
+    documentation_url: https://scglue.readthedocs.io/
   arguments:
     - name: --multiomics_rna
       __merge__: ../../api/file_multiomics_rna_h5ad.yaml
@@ -63,21 +62,21 @@ functionality:
       type: integer
       direction: input
       default: 4
-  test_resources:
-    - type: python_script
-      path: /src/common/component_tests/run_and_check_output.py
-    - path: /resources/grn-benchmark
-      dest: resources/grn-benchmark
+
   resources:
     - type: python_script
       path: script.py
+    - path: main.py
 
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.4
-    setup:
-      - type: python
-        packages: [  ]
+    image: janursa/scglue:19-08-2024:
+    # image: nvcr.io/nvidia/pytorch:24.06-py3
+    # setup:
+    #   - type: python
+    #     packages: [ scglue==0.3.2, pyscenic==0.12.1, numpy==1.23.4, scanpy, networkx, pyarrow, cytoolz, scikit-misc, cuda-python]
+    #   - type: apt
+    #     packages: [bedtools]
 
   - type: native
   - type: nextflow